tellurium.tests.sedml package

Submodules

tellurium.tests.sedml.test_archive module

Test class to check issues with single archives.

tellurium.tests.sedml.test_archive.test_single_omex(tmpdir)

tellurium.tests.sedml.test_data module

Testing of SED-ML data support, i.e., DataDescription.

tellurium.tests.sedml.test_data.parseDataDescriptions(sedml_path)

Test helper functions.

Tries to parse all DataDescriptions in the SED-ML file.

tellurium.tests.sedml.test_data.setup_module(module)

setup any state specific to the execution of the given module.

tellurium.tests.sedml.test_data.teardown_module(module)

teardown any state that was previously setup with a setup_module method.

tellurium.tests.sedml.test_data.test_load_csv()

tellurium.tests.sedml.test_data.test_load_csv_parameters()

tellurium.tests.sedml.test_data.test_load_numl()

tellurium.tests.sedml.test_data.test_load_numl_1D()

tellurium.tests.sedml.test_data.test_load_numl_2D()

tellurium.tests.sedml.test_data.test_load_numl_2DRC()

tellurium.tests.sedml.test_data.test_load_tsv()

tellurium.tests.sedml.test_data.test_omex_csv_parameters(tmpdir)

tellurium.tests.sedml.test_data.test_omex_jws_adlung2017_fig2gl(tmpdir)

tellurium.tests.sedml.test_data.test_omex_plot_csv(tmpdir)

tellurium.tests.sedml.test_data.test_omex_plot_csv_with_model(tmpdir)

tellurium.tests.sedml.test_data.test_omex_plot_numl(tmpdir)

tellurium.tests.sedml.test_data.test_omex_plot_numl_with_model(tmpdir)

tellurium.tests.sedml.test_data.test_parse_csv()

tellurium.tests.sedml.test_data.test_parse_csv_parameters()

tellurium.tests.sedml.test_data.test_parse_numl()

tellurium.tests.sedml.test_data.test_parse_numl_1D()

tellurium.tests.sedml.test_data.test_parse_numl_2D()

tellurium.tests.sedml.test_data.test_parse_numl_2DRC()

tellurium.tests.sedml.test_data.test_parse_tsv()

tellurium.tests.sedml.test_kisao module

Testing the support of KISAO terms for SED-ML simulations.

test_sedml_phrasedml.py : phrasedml based tests. test_sedml_kisao.py : SED-ML kisao support test_sedml_omex.py : SED-ML tests based on Combine Archives test_sedml_sedml.py : sed-ml tests

class tellurium.tests.sedml.test_kisao.KisaoSedmlTestCase(methodName='runTest')

Bases: unittest.case.TestCase

checkKisaoAlgorithmParameter(inline_omex, kisao, name, value)

Helper function for checking kisao parameter.

checkKisaoIntegrator(inline_omex, kisao, name)

Helper function for checking kisao integrator.

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_kisao_absolute_tolerance_1()

test_kisao_absolute_tolerance_2()

test_kisao_adams()

test_kisao_bdf()

test_kisao_cvode_1()

test_kisao_cvode_2()

test_kisao_cvode_3()

Default of uniform is cvode.

test_kisao_cvode_4()

Default of onestep is cvode.

test_kisao_gillespie_1()

test_kisao_gillespie_2()

test_kisao_gillespie_3()

Default of uniform_stochastic is gillespie.

test_kisao_initial_time_step_1()

test_kisao_initial_time_step_2()

test_kisao_maximum_adams_order_1()

test_kisao_maximum_adams_order_2()

test_kisao_maximum_bdf_order_1()

test_kisao_maximum_bdf_order_2()

test_kisao_maximum_iterations_1()

test_kisao_maximum_iterations_2()

test_kisao_maximum_num_steps_1()

test_kisao_maximum_num_steps_2()

test_kisao_maximum_time_step_1()

test_kisao_maximum_time_step_2()

test_kisao_minimum_damping_1()

test_kisao_minimum_damping_2()

test_kisao_minimum_time_step_1()

test_kisao_minimum_time_step_2()

test_kisao_relative_tolerance_1()

test_kisao_relative_tolerance_2()

test_kisao_rk45_1()

test_kisao_rk45_2()

test_kisao_rk4_1()

test_kisao_rk4_2()

test_kisao_seed_1()

test_kisao_seed_2()

test_kisao_variable_step_size_1()

test_kisao_variable_step_size_2()

tellurium.tests.sedml.test_omex module

Test that Combine archives can be executed successfully.

class tellurium.tests.sedml.test_omex.OmexTestCase(methodName='runTest')

Bases: unittest.case.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_000_CombineArchiveShowCase_o()

Test failes if Exception in execution of f.

test_006_ho1995_fig3_s()

Test failes if Exception in execution of f.

test_007_beuke2017_fig6_s()

Test failes if Exception in execution of f.

test_008_roy2010_fig3_s()

Test failes if Exception in execution of f.

test_011_essunger1994_fig8_s()

Test failes if Exception in execution of f.

test_017_martins2016_figev3a_s()

Test failes if Exception in execution of f.

test_018_martins2016_fig6_s()

Test failes if Exception in execution of f.

test_022_kolodkin2010_figure2b_s()

Test failes if Exception in execution of f.

test_025_essunger1994_fig4_s()

Test failes if Exception in execution of f.

test_029_ouattara2008_fig3_s()

Test failes if Exception in execution of f.

test_034_jones2002_fig2_s()

Test failes if Exception in execution of f.

test_036_iwami2012_fig3_s()

Test failes if Exception in execution of f.

test_044_bajaria2002_fig2_s()

Test failes if Exception in execution of f.

test_053_hernandezvargas2013_s()

Test failes if Exception in execution of f.

test_055_pankavich2016_fig1_s()

Test failes if Exception in execution of f.

test_057_essunger1994_fig5_s()

Test failes if Exception in execution of f.

test_058_fisher2006_fig3a_s()

Test failes if Exception in execution of f.

test_067_fan2014_fig1a_s()

Test failes if Exception in execution of f.

test_074_fraser2002_fig1a_1b_2a_2b_s()

Test failes if Exception in execution of f.

test_075_pankavich2016_fig2_s()

Test failes if Exception in execution of f.

test_077_miao2008_fig1_s()

Test failes if Exception in execution of f.

test_081_chan2004_fig3_s()

Test failes if Exception in execution of f.

test_084_BIOMD0000000144_fig1b_sedml_o()

Test failes if Exception in execution of f.

test_085_BIOMD0000000169_fig5c_sedml_o()

Test failes if Exception in execution of f.

test_086_BIOMD0000000370_fig2_sedml_o()

Test failes if Exception in execution of f.

test_087_BIOMD0000000228_fig4_sedml_o()

Test failes if Exception in execution of f.

test_088_BIOMD0000000005_sedml_o()

Test failes if Exception in execution of f.

test_089_BIOMD0000000409_fig7b_sedml_o()

Test failes if Exception in execution of f.

test_090_BIOMD0000000150_fig1b_sedml_o()

Test failes if Exception in execution of f.

test_091_BIOMD0000000297_fig3_sedml_o()

Test failes if Exception in execution of f.

test_092_BIOMD0000000208_fig3a_sedml_o()

Test failes if Exception in execution of f.

test_093_BIOMD0000000193_fig2b_sedml_o()

Test failes if Exception in execution of f.

test_094_BIOMD0000000195_fig8a_sedml_o()

Test failes if Exception in execution of f.

test_095_BIOMD0000000216_fig2c_sedml_o()

Test failes if Exception in execution of f.

test_096_BIOMD0000000008_sedml_o()

Test failes if Exception in execution of f.

test_097_MODEL3897771820_fig8_sedml_o()

Test failes if Exception in execution of f.

test_098_BIOMD0000000186_fig3a_sedml_o()

Test failes if Exception in execution of f.

test_099_BIOMD0000000107_fig13_sedml_o()

Test failes if Exception in execution of f.

test_100_BIOMD0000000242_fig2_sedml_o()

Test failes if Exception in execution of f.

test_101_BIOMD0000000107_fig9_sedml_o()

Test failes if Exception in execution of f.

test_102_BIOMD0000000187_fig3b_sedml_o()

Test failes if Exception in execution of f.

test_103_BIOMD0000000056_fig2_sedml_o()

Test failes if Exception in execution of f.

test_104_BIOMD0000000194_fig2b_sedml_o()

Test failes if Exception in execution of f.

test_105_BIOMD0000000110_fig6B_sedml_o()

Test failes if Exception in execution of f.

test_106_BIOMD0000000087_fig5_sedml_o()

Test failes if Exception in execution of f.

test_107_BIOMD0000000168_fig3a_sedml_o()

Test failes if Exception in execution of f.

test_108_BIOMD0000000007_fig_2a_sedml_o()

Test failes if Exception in execution of f.

test_109_BIOMD0000000111_fi4_sedml_o()

Test failes if Exception in execution of f.

test_110_BIOMD0000000181_fig12_sedml_o()

Test failes if Exception in execution of f.

test_111_BIOMD0000000109_sf2a_sedml_o()

Test failes if Exception in execution of f.

test_112_BIOMD0000000207_c_sedml_o()

Test failes if Exception in execution of f.

test_113_BIOMD0000000196_sedml_o()

Test failes if Exception in execution of f.

test_114_BIOMD0000000406_fig7c_sedml_o()

Test failes if Exception in execution of f.

test_115_BIOMD0000000265_fig2_sedml_o()

Test failes if Exception in execution of f.

test_116_BIOMD0000000003_sedml_o()

Test failes if Exception in execution of f.

test_117_BIOMD0000000004_sedml_o()

Test failes if Exception in execution of f.

test_118_BIOMD0000000007_fig_2a_b_sedml_o()

Test failes if Exception in execution of f.

test_119_BIOMD0000000207_ab_sedml_o()

Test failes if Exception in execution of f.

test_120_BIOMD0000000003_fig4_sedml_o()

Test failes if Exception in execution of f.

test_126_L1V3_ikappab_o()

Test failes if Exception in execution of f.

test_130_L1V3_repressilator_o()

Test failes if Exception in execution of f.

test_136_brusselator_s()

Test failes if Exception in execution of f.

test_137_parameterScan2D_o()

Test failes if Exception in execution of f.

test_138_case_04_o()

Test failes if Exception in execution of f.

test_139_lorenz_o()

Test failes if Exception in execution of f.

test_140_case_08_o()

Test failes if Exception in execution of f.

test_141_case_06_o()

Test failes if Exception in execution of f.

test_142_BIOMD0000000003_s()

Test failes if Exception in execution of f.

test_143_BIOMD0000000012_s()

Test failes if Exception in execution of f.

test_144_repeatedStochastic_o()

Test failes if Exception in execution of f.

test_146_case_01_o()

Test failes if Exception in execution of f.

test_147_BorisEJB_s()

Test failes if Exception in execution of f.

test_148_oneStep_o()

Test failes if Exception in execution of f.

test_149_BorisEJBos_s()

Test failes if Exception in execution of f.

test_150_BM12_s()

Test failes if Exception in execution of f.

test_151_EllowitzRepressilator_s()

Test failes if Exception in execution of f.

test_152_case_10_o()

Test failes if Exception in execution of f.

test_153_BorisEJBsteady_s()

Test failes if Exception in execution of f.

test_154_BIOMD0000000139_s()

Test failes if Exception in execution of f.

test_155_parameterScan1D_o()

Test failes if Exception in execution of f.

test_156_case_09_o()

Test failes if Exception in execution of f.

test_157_ClockSedML_s()

Test failes if Exception in execution of f.

test_158_repressilator_o()

Test failes if Exception in execution of f.

test_159_case_11_o()

Test failes if Exception in execution of f.

test_160_case_05_o()

Test failes if Exception in execution of f.

test_161_JanaWolf_s()

Test failes if Exception in execution of f.

test_162_sedmlCurienJWS_s()

Test failes if Exception in execution of f.

test_163_case_02_o()

Test failes if Exception in execution of f.

test_165_case_07_o()

Test failes if Exception in execution of f.

test_166_case_03_o()

Test failes if Exception in execution of f.

test_167_BIOMD0000000140_s()

Test failes if Exception in execution of f.

test_168_specificationL1V2_s()

Test failes if Exception in execution of f.

test_169_case_12_o()

Test failes if Exception in execution of f.

test_170_sedMLBIOM21_s()

Test failes if Exception in execution of f.

test_171_miase_s()

Test failes if Exception in execution of f.

tellurium.tests.sedml.test_omex.f_omex_filter(filename)

tellurium.tests.sedml.test_omex.ftest_generator(filePath)

tellurium.tests.sedml.test_omex.test(self=None)

Test failes if Exception in execution of f.

tellurium.tests.sedml.test_phrasedml module

Testing phrasedml.

test_sedml_phrasedml.py : phrasedml based tests. test_sedml_kisao.py : SED-ML kisao support test_sedml_omex.py : SED-ML tests based on Combine Archives test_sedml_sedml.py : sed-ml tests

class tellurium.tests.sedml.test_phrasedml.PhrasedmlTestCase(methodName='runTest')

Bases: unittest.case.TestCase

Testing execution and archives based on phrasedml input.

run_example(a_str, p_str)

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_1Model1PhrasedML()

Minimal example which should work.

test_1Model2PhrasedML()

Test multiple models and multiple phrasedml files.

test_2Model1PhrasedML()

Test multiple models and multiple phrasedml files.

test_2Model2PhrasedML()

Test multiple models and multiple phrasedml files.

test_case_01()

test_case_02()

test_case_03()

test_case_04()

test_case_05()

test_case_06()

test_case_07()

test_case_08()

test_case_09()

test_case_10()

test_case_11()

test_case_12()

test_execute()

Test execute.

test_exportAsCombine()

Test exportAsCombine.

test_lorenz()

test_oneStep()

test_parameterScan1D()

test_parameterScan2D()

test_repeatedStochastic()

test_repressilator()

test_simpletimecourse()

tellurium.tests.sedml.test_sedml module

Test all the SED-ML files if code can be generated,

test_sedml_phrasedml.py : phrasedml based tests. test_sedml_kisao.py : SED-ML kisao support test_sedml_omex.py : SED-ML tests based on Combine Archives test_sedml_sedml.py : sed-ml tests

class tellurium.tests.sedml.test_sedml.SEDMLTestCase(methodName='runTest')

Bases: unittest.case.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

single_check(f_sedml)

Test if python code can be generated from the SED-ML file.

Parameters:f_sedml – Returns: Return type:

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_app2sim()

Test app2sim SED-ML example.

test_asedml3repeat()

Test asedml3repeat SED-ML example.

test_asedmlComplex()

Test asedmlComplex SED-ML example.

test_constant_maybe()

Test constant_maybe SED-ML example.

test_via_sedml_string()

Test SED-ML from string.

tellurium.tests.sedml.test_tesedml module

class tellurium.tests.sedml.test_tesedml.OmexSedmlTestCase(methodName='runTest')

Bases: unittest.case.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_omex_combineArchiveToPython()

test_omex_executeCombineArchive()

Module contents